Screenshot of the day: Proteomics apologizes to PubMed’s readership.

Last time I said: Although the paper was retracted from the online version of Proteomics, you can still make historical screenshots on the PubMed version. Now the chance is over. But what is really funny: finally, PubMed ‘Related Links’ algorithm gives us the proper context of the Warda-Han-Mighty paper, just take a look at the… Continue reading Screenshot of the day: Proteomics apologizes to PubMed’s readership.

Nature’s Great Beyond on the Warda-Han-Proteomics-Creator paper

Peer review, ‘a mighty creator’ and an almighty row However the paper was only retracted for “a substantial overlap of the content of this article with previously published articles in other journals.”, not for the strange “mighty creator” line. Peer review isn’t perfect but you’d hope it would catch something like this.

Warda speaks: “We say the truth, I not burrow any sentences from others.”

The Warda-Han-Proteomics saga continues and finds its way to the show/entertainment business. We’ve already listened to Han, now it’s time for Warda to speak, which he did in an email to James Randerson over at the Guardian Science blog, which makes think (indeed ‘rethink’ as W suggests) that the Warda-Han pair is probably the Laurel… Continue reading Warda speaks: “We say the truth, I not burrow any sentences from others.”

The Warda-Han-Proteomics scandal: fingerprints of plagiarism, too

We have now a well-developed and sad case example of irresponsible scientific editing and publishing: the Warda-Han advanced online paper by the academic journal Proteomics: Mitochondria, the missing link between body and soul: Proteomic prospective evidence. What started as an abstract-based hunch and question about the quality of a recent review, addressed to and amplified… Continue reading The Warda-Han-Proteomics scandal: fingerprints of plagiarism, too

The fingerprints of a mighty creator in Proteomics, impact factor >5

Creationism/intelligent design is not really an issue for me as I am a biologist working with mitochondria and stem cells, also a life extension supporter, whose angle on things and projections are based on the recent advancements in science and technology. As far as I know, creationism/ID neither suggests any new experiments or heuristic solutions… Continue reading The fingerprints of a mighty creator in Proteomics, impact factor >5

Can you tell a good article from a bad based on the abstract and the title alone?

Many times people only have access to the abstract of peer-review articles, and nothing more. There are different abstract styles (sometimes they’re going too far or on the contrary) in the literature and I’d be curious to hear about your opinion on the following review abstract and title. I became interested and suspicious reading these… Continue reading Can you tell a good article from a bad based on the abstract and the title alone?

Stat freaks, are you ready to play with the SCImago Journal & Country Rank?

Finally the Google PageRank algorithm, the core analysis tool of the current web is back to where its idea is originated from, scientific citation analysis. The recently launched SCImago Journal & Country Rank database uses an algorithm very similar to PageRank. It has a new metric: the SCImago Journal Rank (SJR). According to Nature: A… Continue reading Stat freaks, are you ready to play with the SCImago Journal & Country Rank?

23andMe on the biparental inheritance of mitochondrial DNA and more

In my former blog post inF.A.Q. for 23andMe: what if I have mitochondrial DNA from Pa? I meditated on 23andMe‘s capability of detecting paternal mitochondrial DNA in their customers’ saliva with their Illumina microarray chips scanning around 2000 mitochondrial single nucleotide variants. Published here the initial answer of the 23andMe Editorial Team to this fairly… Continue reading 23andMe on the biparental inheritance of mitochondrial DNA and more

Unofficial and hypercritical peer review of a paper on p53’s role in hESC regulation

Once I wrote shortly about the following peer review paper which was popped out of my PubMed feeds to draw some attention to it: Han Qin, Tianxin Yu, Tingting Qing, Yanxia Liu, Yang Zhao, Jun Cai, Jian Li, Zhihua Song, Xiuxia Qu, Peng Zhou, Jiong Wu, Mingxiao Ding, Hongkui Deng Regulation of apoptosis and differentiation… Continue reading Unofficial and hypercritical peer review of a paper on p53’s role in hESC regulation

BioMed Search relaunched

BioMed Search, the Google-like BioMedical Image Search Engine is alive after a long off period as it was relaunched about 1 month ago. Current informal science communication in the lab (say in lab meetings or in journal clubs) is centered around interpreting figures. BioMed Search catches somehow the essence of this communication with indexing the… Continue reading BioMed Search relaunched

Meet the nodes, “clustered hubs” and links of clathrin-mediated endocytosis

Network biology is a way to integrate fragmented benchwork data in order to understand complex biological phenomena. In a recent Nature paper, entitled Integrating molecular and network biology to decode endocytosis Cambridge (UK) researchers authors Eva Schmid and Harvey McMahon of MRC, Cambridge give a good example of a predictive and experimentally useful systems biology… Continue reading Meet the nodes, “clustered hubs” and links of clathrin-mediated endocytosis

The role of Journal Club in lab life and how to move the genre to the web

Regular (daily, weekly) Journal Clubs are crucially important events in the life of labs. Reviewing other labs’ results is a way to get synchronized with all the data accumulated by a particular subdiscipline. Moreover it is the most obvious everyday form (conferences are not that frequent) of secondary peer review of the given paper, when… Continue reading The role of Journal Club in lab life and how to move the genre to the web

Journal Club slideshow: MSC lung repair via lung-derived microvesicles

Embedded is my classical style (no design, based on the figure section, Powerpoint instead of Keynote) Journal Club presentation on the following paper with the help of SlideShare: Alteration of Marrow Cell Gene Expression, Protein Production and Engraftment into Lung by Lung-derived Microvesicles: A Novel Mechanism for Phenotype Modulation by Aliotta JM, Sanchez-Guijo FM, Dooner… Continue reading Journal Club slideshow: MSC lung repair via lung-derived microvesicles

The Niche: The Stem Cell Blog hosted by Nature Stem Cell Reports

How many fine niche stem cell blogs do you know? 4-3-2-1? How many with an attractive, easy to remember name? 0? Good, short, actual and proper blog names are rare. Let me introduce you The Niche which intends to become THE Stem Cell Blog in the niche of the niches. It is the newest Nature… Continue reading The Niche: The Stem Cell Blog hosted by Nature Stem Cell Reports

Nature Reports Stem Cells is live from now on…for stem cell enthusiasts

No more waiting: Nature Reports Stem Cells (NRSC) launched today, and so finally there is a fully web native, scientifically high-end (naturally), freely accessible, all-in-one stem cell research hub site for everyone (especially for the researchers) to read, share, contribute and turn the acquired insights back into new experiments, policies, ethics, businesses and clinical trials.… Continue reading Nature Reports Stem Cells is live from now on…for stem cell enthusiasts

Forget about submitting your scientific papers written in Word 2007

Wow, I feel fresh air, although I am not sure whether the following news is a beginning of any deeper changes or not: From Science Authors Guideline: “Because of changes Microsoft has made in its recent Word release that are incompatible with our internal workflow, which was built around previous versions of the software, Science… Continue reading Forget about submitting your scientific papers written in Word 2007

Editing my doctoral thesis on stem cells in a blog: Why not?

OK folks, after reading the official rules about how to get and manage a doctoral thesis, and after speaking with my supervisor asking for his permission, I’ve decided to edit my ongoing doctoral thesis in Pimm. Or at least the introduction of it, which is intended to be no other than a review-like summary of… Continue reading Editing my doctoral thesis on stem cells in a blog: Why not?

Informational emergency in the operating room: does it count as a right?

I found this exciting case in the book (yes, I am still reading those) of Lancet editor-in-chief Richard Horton called: Second Opinion: Doctors, Diseases and Decisions in Modern Medicine “Surgery is all about action, not reflection. But information is sometimes critical, even in the operating room. In 2002, surgeons in Australia were working frantically to… Continue reading Informational emergency in the operating room: does it count as a right?

Cell’s Superhero Cover: the role of comics in science popularization

I’ve just realized how cool is Cell magazine May 4 issue’s cover (the one with the Scientist Enter the Blogosphere report by Laura Bonetta) with the S-nitrosothiol superhero T-shirt. This substance may have some therapeutic utility in diseases such as heart failure and asthma. Illustration: Cell and me this morning. Cartoons are terrific education tools,… Continue reading Cell’s Superhero Cover: the role of comics in science popularization

Bone marrow stem cells, the great cancer pretenders?

In the lack of subscription to Stem Cells, I could not download the whole article or the subscription restricted supplemental data (at Stem Cells it seems people haven’t heard of free supplemental information) but this story is really interesting: Bone Marrow Contributes to Epithelial Cancers in Mice and Humans as Developmental Mimicry In brief: in… Continue reading Bone marrow stem cells, the great cancer pretenders?

2 models of embryonic and adult blood formation: Figure by Ueno and Weissman

If you have previously thought (in your spare time) that the conventional wisdom concerning blood formation is that the yolk sac’s embryonic blood-forming cells serve only the embryo, while the source of adult blood-forming stem cells is the region called aorta-gonad-mesonephros (AGM), it’s time to think it again due the elegant experiments of Samokhalov et… Continue reading 2 models of embryonic and adult blood formation: Figure by Ueno and Weissman

Looking for user friendly, attractive peer review article titles….

These two titles are freshly out of my feed readers: B-type natriuretic peptide inhibited angiotensin II-stimulated cholesterol biosynthesis, cholesterol transfer and steroidogenesis in primary human adrenocortical cells. and In vivo expression of human ATP:cob(I)alamin adenosyltransferase (ATR) using recombinant adeno-associated virus (rAAV) serotypes 2 and 8. How user friendly these titles are? Let’s examine me: Theoretically… Continue reading Looking for user friendly, attractive peer review article titles….

Free Nature Reviews Neuroscience Issue in May

From the Nautilus blog by Maxine Clarke: “Nature Reviews Neuroscience is the no. 1 monthly review journal in neuroscience, with an impact factor of 20.951. In May, online access to the entire issue is free.” I would like to offer these articles which could be of interest for stem cell biologists: Research Highlights Neurogenesis: Single… Continue reading Free Nature Reviews Neuroscience Issue in May

Stories from my PubMed feeds: hESCs, p53, apoptosis and differentiation

Short peer-review storytelling : One big technical problem of human embryonic stem cells (hESCs) (in contrast to mouse embryonic stem cells) that hESCs normally undergo high rates of spontaneous apoptosis and differentiation, making them difficult to maintain in culture. Now we are getting to know a bit more on the molecular background of these processes.… Continue reading Stories from my PubMed feeds: hESCs, p53, apoptosis and differentiation

Blogxperiment: What are the good ways to summarize peer-review articles?

In future posts I’d like to do a blogxperiment based on comments feedback. My general question is: What is the best way to summarize peer-review articles for a more general readership and transmit scholarly knowledge and literature? What are the opportunities used in blog posts? Figures, abstracts, dense citations, other summarize options, journalist lingo, superficial… Continue reading Blogxperiment: What are the good ways to summarize peer-review articles?

Nature Publishing Editor on the idea of a public scientific multimedia site

Maxine Clarke, Publishing Executive Editor of Nature and blogger of Peer-to-Peer got interested in the problem of “supporting information” and in the idea of an open access, peer-review supporting information aggregator website. She shared with me her valuable thoughts and informations by mail, from which I now publish parts with the permission of Maxine Clarke… Continue reading Nature Publishing Editor on the idea of a public scientific multimedia site

Let’s make ‘supplementary’ peer-review scientific videos free and youtubish!

In the last post on “supporting information” section I claimed that the problematic status of supporting information comes from the heterogeneity of its data, on the one hand genuine online multimedial files, on the other hand “paperlike” data. Big differences also occur concerning the importance of the data. The source of the heterogeneity is the… Continue reading Let’s make ‘supplementary’ peer-review scientific videos free and youtubish!

The problem of online “supporting information” in peer-review articles

Most articles published in peer-review journals are organized into the following sections: Title, Authors, Affiliations, Abstract, Introduction, Results, Discussion, Materials and Methods (it could stand before Results), Acknowledgments, References, and Figure Legends. But every current researcher in the field of life sciences has already had some time with the stepsibling of those full blooded formal… Continue reading The problem of online “supporting information” in peer-review articles

JoVE 2.0 makes science social and pop: video sharing, comments, interviews

You must definitely check the completely redesigned, upgraded JoVE website to see the enhanced present of online science! Journal of Visualized Experiments (JoVE) is an online journal publishing visualized (video-based) biological research studies. It was launched in November, 2006 and now due to the hard work and entrepreneurial spirit of editor Moshe Pritsker, web developer… Continue reading JoVE 2.0 makes science social and pop: video sharing, comments, interviews

Cord blood stem cell therapy without immune suppression?

The first scientific review of the rationale for the practical use of umbilical cord stem cells without the use of immune suppression was published in the Journal of Translational Medicine and it is freely available: “the authors propose that expanding the use of cord blood to non-preconditioned adult recipients for regenerative purposes would be a… Continue reading Cord blood stem cell therapy without immune suppression?

Early progenitor cell number as organ size determinant: pancreas

Developmental biology is the gold mine of stem cell biology. A pioneer, but elegant quantitative cell biology paper was published in Nature advance online publication on 28, January 2007 by U.S. researchers Stanger, Tanaka, Melton along developmental lines. Based on the strict regulation of vertebrate development it was thought that extrinsic or systemic signals, growth… Continue reading Early progenitor cell number as organ size determinant: pancreas

How to filter and read PubMed articles through RSS feeds?

How many people out of you, life scientists, are regularly updating their PubMed searches through RSS feeds? According to the Read/Write Read Blog 2006 Web Technology Trends “While 2006 can’t be seen as the breakthrough year for RSS in the mainstream, we will probably see RSS bloom in 2007”. It’s January, 2007, so let’s upgrade… Continue reading How to filter and read PubMed articles through RSS feeds?

Nature Medicine 2.0 alarms by its editor in chief

Oops, the folks at Nature Publishing Group are more and more watching us, the people of the second-generation Internet, you know the two point oh. Recently, the editor chief of Nature Medicine (impact factor 28.878 in 2005), Juan Carlos Lopez wrote and editorial and even a blog post concerning “what is the Web 2.0–driven scientific… Continue reading Nature Medicine 2.0 alarms by its editor in chief

Big volume brain repair through escaped neural stem cells in mice

In the 15th, December Cell issue Kuo et al. published a study according to which “mice whose brains were severely damaged by loss of the genes “Numb” and “Numblike” in one region just after birth showed substantial mending within weeks. The researchers attributed that repair to neural stem cell “escapees” that had somehow retained or… Continue reading Big volume brain repair through escaped neural stem cells in mice

Google Scholar: story, goal, founding engineer and team

Probably you people in life sciences and biomedical fields with open eyes to current academic and advanced web developments (like BioMed Search and JovE) have happened to meet and try sometimes Google Scholar, Google’s own scholarly search engine, leaving PubMed for a moment behind. Now here is an interview with Scholar’s founding engineer, Anurag Acharya… Continue reading Google Scholar: story, goal, founding engineer and team

The image of science: Google-like Biomedical Image Search Engine for pros

Check out the brand new BioMed Search, it is fantastic, currently over 1 million images have been indexed from peer-review journals in biomedical fields and more is on its way. BioMed Search has been created by Alex Ksikes, currently a Ph.D. candidate in Computer Science with focus in Computational Learning Theory at the University of… Continue reading The image of science: Google-like Biomedical Image Search Engine for pros

JoVE stats: blogosphere and Nature News traffic before official launch

The first official issue of the new biological video protocol site JoVE or Journal of Visualized Experiments will be available today 11 pm EST, November 30, 2006. The graph shows November traffic in term of unique visitors, first 2.5 weeks mainly uploaders, authors, editors and editors’ friends used the page, from 17th there was a… Continue reading JoVE stats: blogosphere and Nature News traffic before official launch

Human heart mitochondria and nitric oxide production: hard work

I’ve almost missed the publication of an article by our group back home, in Budapest which is my first real first author peer-review article published in Life Sciences, impact factor, 2.512 as of 2005. The peer-review process was hard (illustration: me under the hood) and bloody, because it is a negative result, so you have… Continue reading Human heart mitochondria and nitric oxide production: hard work

hESCs derived from single blastomere by Lanza et al.: second trial in Nature with success

In science you can always correct yourself. In stem cell research it is of utmost importance to correct what you’re claiming, if you’ve claimed it not accurately enough before. Now in November 23 Nature magazine the Lanza group has a corrected manuscript on Human embryonic stem cell lines derived from single blastomeres on the possibility… Continue reading hESCs derived from single blastomere by Lanza et al.: second trial in Nature with success